Pervasive problems - marked by chaotic record-keeping, rampant human error and ineffective oversight - run deeper at Harris County's probation department than courthouse insiders may have imagined, according to thousands of documents obtained by the Houston Chronicle.

After a jarring court hearing last month cast doubt on the accuracy of the department's 300,000 annual drug tests, its director and two lieutenants have resigned, the District Attorney's Office and some judges have shunned all lab results, and state officials have launched an investigation.

"There was no part of the process that was exempt from error after error after error," said Lisa Andrews, the lawyer who put the agency on trial for three days while defending a probationer. "There were errors from the time someone walked in and showed their identification all the way until the data was uploaded to the county's computer."

Among the problems identified from internal probation department records:

» Hundreds of probationers' test results were botched, with flawed files going uncorrected for weeks or even months; some people were jailed or hauled into court based on positive samples that were not theirs or because they were listed as having skipped test appointments they actually attended.

» Scores of samples had to be destroyed because the forms establishing the legal chain of custody were missing or incomplete; one supervisor testified this chain "has more holes than Swiss cheese."

» Many probationers had to revisit offices to be retested for myriad reasons, including plumbing problems at the facility, a lack of female workers to monitor women probationers or because the lab ran out of gloves to handle samples.

'Scientific screw-ups'

Some of those issues were known to agency officials years before Andrews' subpoenas arrived in July. In September 2009, managers at one office pleaded for additional staff, noting long wait times and problems with accuracy.

"South Region has experienced some problems with the collection of specimens by personnel other than the designated employee," they wrote. "These problems highlight the need for competent specifically trained staff to be assigned to this position. Mistakes of this magnitude cannot be tolerated as it could affect the client's freedom and possibly leave the department open to litigation, liability and credibility questions."

Andrews and other lawyers said they were appalled by revelations of misconduct at the probation department, but not surprised.

The hearing in state District Judge Denise Collins' court ended Aug. 27, with Collins calling for the resignation of the head of the department and issuing a moratorium on test results until they can be trusted. A day later, the Harris County District Attorney's Office announced it would stop using the results as evidence in Houston's 37 criminal courts.

Within days, department head Paul Becker and two of his top lieutenants resigned from the agency, which is funded mostly by state dollars and overseen by the criminal court judges. Remaining agency employees have refused to comment despite repeated calls and emails.

The judges, acting as a board, announced Friday they are seeking a temporary director to take over immediately.

Whoever takes Becker's job will have to grapple with a slew of issues staffers noted as early as 2007, and were common topics by 2009.

100 positives a day

In a county as large as Harris, the drug testing program is understandably massive, yet simple. About 1,000 people report each day to several regional offices to urinate in cups. Test strips on the cups indicate positive or negative results for various drugs. The presumptive positives, about 100 a day, are sent to an outside lab for confirmation. Those samples are tested again and the results are uploaded to client's files, which are accessed by probation officers who forward results to each probationer's judge for review.

That process, however, was rife with human errors.

There were at least 644 requests to "unlock" probationers' files for corrections or updates between 2008 and 2012, with supervisors sometimes scrambling to correct records the day before a probationer's court hearing or, failing that, in front of the judge. Some samples accidentally were thrown away, including at least one case in which a man admitted to staff he was going to test positive.

Shipments of presumptive positives sent to the lab for confirmation sometimes leaked, and at least one arrived almost empty; shipping protocols later were changed.

One man was jailed after giving a sample at a branch that was not his assigned location.

Samples not secured

Errors were so common that probation staff turned conversational in emails about them, asking, "Was this another fat finger or what," or acknowledging, "Am real confused now Lol..." and, "I clicked to(sic) fast on his record."

To be admitted as evidence, the sample, test and result must be accounted for at each step in the process. This chain of custody is a safeguard against evidence tampering and is the standard for physical evidence in criminal court. Chain-of-custody errors were common at the agency.

An April 2010 internal audit of the east regional office found the lab and the restrooms where samples were collected remained unlocked, and the key for the locked sample refrigerator sitting right next to it.

In one incident, a receptionist doubling as a technician did not record a probationer's test result before returning to the front desk. A colleague noticed the sample had registered positive and shipped it to the lab for confirmation. When the receptionist later could not find the sample, she assumed it was negative and entered the results as such, leaving a positive and a negative test in the client's file for the same day.

Some cups sat in the refrigerator for months before being tested.

Managers sought fixes, such as requiring technicians to sign on with a password to enter test results in 2009. Some technicians, however, later complained colleagues had committed errors under their names: "Someone has used my password and computer and done this I don't know," one wrote in February. "I need my name took(sic) off of this."

Unique identifiers

Steve Harris, lab director for the county's current lab vendor, One Source Toxicology, said chain of custody issues seemed to be the department's biggest problem.

Harris said many of the agency's troubles stemmed from using only one unique identifier - a date of birth, for example - for each urinalysis sample. Most probation departments in Texas, he said, use three or even four, to ensure one typing error does not land the wrong person in jail.

Data entry mistakes happen, Harris said. In the past 18 months, his lab has tested about 40,000 samples with 31 errors, which were caught because of multiple identifiers.

At the urging of Harris and some staff, the agency now uses two, and the system started catching mistakes in July.

The issues have long been visible for those who wanted to see them, said Donald Martin, a supervisor who seemed to know the most about the problems and why they were not fixed. Martin testified he could not trust that any of the positive test results was "truly a positive."